[BioPython] Performing sequence alignments, etc.

[Caitlin]

Thanks Peter. The genomes are viral. I'll definitely read that
tutorial.
Your help is very appreciated.

~Caitlin

--- Peter <biopython at maubp.freeserve.co.uk> wrote:

> Caitlin wrote:
> > Hi all.
> > 
> > I'm relatively new to the field of bioinformatics and I'm trying to
> > perform a multiple sequence alignment on 5-6 sequences (fasta
> format -
> > dna sequences). I'd like the output to be formatted in the
> following
> > manner (clustalw standalone output):
> 
> For reading and writing Clustalw alignment files, you could either
> use 
> Bio.SeqIO (format name "clustal") or the Bio.Clustalw module.
> http://biopython.org/wiki/SeqIO
> 
> > When one more more nucleotides columns are identical, clustalw
> displays
> > an asterisk. If not, a blank space is displayed. Is this a standard
> > feature of BioPython?
> 
> There is an example of Clustalw output online here - note there can
> also 
> be a column of numbers on the right hand side (not shown here):
> http://www.bioperl.org/wiki/ClustalW_multiple_alignment_format
> 
> It sounds like you are describing the simple consensus string which 
> clustalw outputs under the alignment (using *:. and space).
> 
> Biopython has a SummaryInfo object which can calculate simple
> consensus 
> sequences (see the tutorial). Perhaps this would be close to what you
> 
> want to do.
> 
> > Also, I'm evaluating several sequences but I'd like to obtain the
> most
> > recent complete genomes possible from various countries. Is there a
> > convenient source to use (GenBank?) if I don't know the accession
> > numbers?
> 
> What sort of Genomes? Bacteria? Vertebrates?  You could start by
> having 
> a look at any of the EMBL, NCBI/GenBank or the Japanese DDBJ (these 
> three are kept in sync with each other).
> 
> Biopython has quite a nice interface for searching and downloading 
> sequences from GenBank (again, see the tutorial) so that would be my 
> first suggestion.
> 
> Peter
> 
> 
> 
> 


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